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- PDB-5mr5: Ligand-receptor complex. -

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Basic information

Entry
Database: PDB / ID: 5mr5
TitleLigand-receptor complex.
Components
  • GDNF family receptor alpha-2GFRα
  • Neurturin
KeywordsSIGNALING PROTEIN / Complex / Receptor / Signalling / Ligand-receptor complex
Function / homology
Function and homology information


glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / glial cell-derived neurotrophic factor receptor signaling pathway / nerve development / heparan sulfate binding / NCAM1 interactions / neural crest cell migration / extrinsic component of membrane / RET signaling / cell surface receptor protein tyrosine kinase signaling pathway ...glial cell-derived neurotrophic factor receptor activity / glial cell-derived neurotrophic factor receptor binding / glial cell-derived neurotrophic factor receptor signaling pathway / nerve development / heparan sulfate binding / NCAM1 interactions / neural crest cell migration / extrinsic component of membrane / RET signaling / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / receptor tyrosine kinase binding / neuron projection development / MAPK cascade / nervous system development / RAF/MAP kinase cascade / receptor complex / external side of plasma membrane / axon / signaling receptor binding / extracellular region / plasma membrane
Similarity search - Function
Glial cell line-derived neurotrophic factor receptor alpha 2 / Glial cell line-derived neurotrophic factor receptor, alpha 1/2 / Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / Glial cell line-derived neurotrophic factor family / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...Glial cell line-derived neurotrophic factor receptor alpha 2 / Glial cell line-derived neurotrophic factor receptor, alpha 1/2 / Glial cell line-derived neurotrophic factor receptor / GDNF receptor alpha / Glial cell line-derived neurotrophic factor family / GDNF/GAS1 / GDNF/GAS1 domain / GDNF/GAS1 domain / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Mainly Beta
Similarity search - Domain/homology
GDNF family receptor alpha-2 / Neurturin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSandmark, J. / Oster, L. / Aagaard, A. / Roth, R. / Dahl, G.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structure and biophysical characterization of the human full-length neurturin-GFRa2 complex: A role for heparan sulfate in signaling.
Authors: Sandmark, J. / Dahl, G. / Oster, L. / Xu, B. / Johansson, P. / Akerud, T. / Aagaard, A. / Davidsson, P. / Bigalke, J.M. / Winzell, M.S. / Rainey, G.J. / Roth, R.G.
History
DepositionDec 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neurturin
B: Neurturin
C: GDNF family receptor alpha-2
D: GDNF family receptor alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,97125
Polymers71,9624
Non-polymers2,00921
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-210 kcal/mol
Surface area29480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.070, 120.300, 78.670
Angle α, β, γ (deg.)90.00, 98.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neurturin /


Mass: 11706.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRTN / Production host: Escherichia coli (E. coli) / References: UniProt: Q99748
#2: Protein GDNF family receptor alpha-2 / GFRα / GFR-alpha-2 / GDNF receptor beta / GDNFR-beta / Neurturin receptor alpha / NTNR-alpha / RET ligand ...GFR-alpha-2 / GDNF receptor beta / GDNFR-beta / Neurturin receptor alpha / NTNR-alpha / RET ligand 2 / TGF-beta-related neurotrophic factor receptor 2


Mass: 24274.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GFRA2, GDNFRB, RETL2, TRNR2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: O00451
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 2.0 M ammonium sulfate and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30.3 Å / Num. obs: 60213 / % possible obs: 93.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyalanine model of 2v5e

2v5e


Resolution: 2→30.28 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.158 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24335 2898 5 %RANDOM
Rwork0.20415 ---
obs0.20609 54696 89.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.603 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20.01 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→30.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4708 0 107 318 5133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194926
X-RAY DIFFRACTIONr_bond_other_d00.024450
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9736664
X-RAY DIFFRACTIONr_angle_other_deg3.658310198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6095592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43121.758256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32815826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9541574
X-RAY DIFFRACTIONr_chiral_restr0.0770.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215568
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021228
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7612.9972374
X-RAY DIFFRACTIONr_mcbond_other1.762.9962373
X-RAY DIFFRACTIONr_mcangle_it2.8464.4862964
X-RAY DIFFRACTIONr_mcangle_other2.8464.4862965
X-RAY DIFFRACTIONr_scbond_it2.3873.4642552
X-RAY DIFFRACTIONr_scbond_other2.3873.4642552
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9045.0593701
X-RAY DIFFRACTIONr_long_range_B_refined6.00823.9895721
X-RAY DIFFRACTIONr_long_range_B_other5.96123.8675614
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 226 -
Rwork0.312 4000 -
obs--89.06 %

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